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He X, Li SM. Genetic methylation in myopia. Ophthalmic Genet 2024; 45:233-234. [PMID: 39044716 DOI: 10.1080/13816810.2024.2381123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 01/30/2024] [Accepted: 01/13/2024] [Indexed: 07/25/2024]
Affiliation(s)
- Xi He
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Shi-Ming Li
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Jiang D, Lin S, Gong Q, Hong J, Wang J, Gao H, Guo Y, Tong F, Zhang Y. PAX6 gene promoter methylation is correlated with myopia in Chinese adolescents: a pilot sutdy. Ophthalmic Genet 2024; 45:219-225. [PMID: 38531548 DOI: 10.1080/13816810.2024.2315152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/02/2023] [Accepted: 02/01/2024] [Indexed: 03/28/2024]
Abstract
PURPOSE A large number of epidemiological studies have shown that myopia is a complex disease involving genetic, environmental, and behavioral factors. The purpose of this study was to explore the role of PAX6 gene methylation in myopia in Chinese adolescents. METHODS Eighty junior high school students were divided into four groups based on their vision test results: mild myopia, moderate myopia, severe myopia, and non-myopia control. The methylation level of PAX6 gene promoter was detected by bisulfate pyrosequencing. RESULTS The methylation level of PAX6 gene in myopia group (8.06% ± 1.43%) was slightly but significantly higher than that in non-myopia controls (7.26% ± 1.17%). In addition, PAX6 gene methylation levels presented a decreasing pattern along with the aggravation of myopia. Post-hoc analysis indicated significant inter-group differences for the mild myopia group and other groups (All p < .05). In the subgroup analysis by gender, the methylation level of PAX6 gene promoter in girls was higher than that in boys (p = .023). The ROC curves showed a high accuracy of PAX6 gene methylation to predict mild myopia (AUC (95% CI) = 0.828 (0.709-0.947), p < .001). CONCLUSIONS The methylation of PAX6 gene might play a role in the onset and progression of myopia in Chinese adolescents. And this could potentially explore the potential molecular mechanisms of juvenile myopia in the future.
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Affiliation(s)
- Danjie Jiang
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Shujuan Lin
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, Putian, China
| | - Qinghai Gong
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Jia Hong
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Jinghui Wang
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Hua Gao
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yanbo Guo
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Feng Tong
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yan Zhang
- Department of School Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
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Hao J, Yang Z, Zhang R, Ma Z, Liu J, Bi H, Guo D. Crosstalk between heredity and environment in myopia: An overview. Heliyon 2024; 10:e29715. [PMID: 38660258 PMCID: PMC11040123 DOI: 10.1016/j.heliyon.2024.e29715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 03/04/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024] Open
Abstract
In recent years, the prevalence of myopia has gradually increased, and it has become a significant global public health problem in the 21st century, posing a serious challenge to human eye health. Currently, it is confirmed that the development of myopia is attributed to the combined action of genes and environmental factors. Thus, elucidating the risk factors and pathogenesis of myopia is of great significance for the prevention and control of myopia. To elucidate the impact of gene-environment interaction on myopia, we used the Pubmed database to search for literature related to myopia. Search terms are as follows: myopia, genes, environmental factors, gene-environment interaction, and treatment. This paper reviews the effects of gene and environmental interaction on myopia.
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Affiliation(s)
- Jiawen Hao
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Zhaohui Yang
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Ruixue Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Zhongyu Ma
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Jinpeng Liu
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Hongsheng Bi
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Jinan, 250002, China
- Shandong Academy of Eye Disease Prevention and Therapy, Jinan, 250002, China
- Shandong Provincial Clinical Research Center of Ophthalmology and Children Visual Impairment Prevention and Control, Jinan, 250002, China
- Shandong Engineering Technology Research Center of Visual Intelligence, Jinan, 250002, China
- Shandong Academy of Health and Myopia Prevention and Control of Children and Adolescents, Jinan, 250002, China
- Medical College of Optometry and Ophthalmology, Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Dadong Guo
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Jinan, 250002, China
- Shandong Academy of Eye Disease Prevention and Therapy, Jinan, 250002, China
- Shandong Provincial Clinical Research Center of Ophthalmology and Children Visual Impairment Prevention and Control, Jinan, 250002, China
- Shandong Engineering Technology Research Center of Visual Intelligence, Jinan, 250002, China
- Shandong Academy of Health and Myopia Prevention and Control of Children and Adolescents, Jinan, 250002, China
- Medical College of Optometry and Ophthalmology, Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
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Radhakrishna U, Sadhasivam S, Radhakrishnan R, Forray A, Muvvala SB, Metpally RP, Patel S, Rawal RM, Vishweswaraiah S, Bahado-Singh RO, Nath SK. Placental cytochrome P450 methylomes in infants exposed to prenatal opioids: exploring the effects of neonatal opioid withdrawal syndrome on health horizons. Front Genet 2024; 14:1292148. [PMID: 38264209 PMCID: PMC10805101 DOI: 10.3389/fgene.2023.1292148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/24/2023] [Indexed: 01/25/2024] Open
Abstract
Background: Neonatal opioid withdrawal syndrome (NOWS), arises due to increased opioid use during pregnancy. Cytochrome P450 (CYP) enzymes play a pivotal role in metabolizing a wide range of substances in the human body, including opioids, other drugs, toxins, and endogenous compounds. The association between CYP gene methylation and opioid effects is unexplored and it could offer promising insights. Objective: To investigate the impact of prenatal opioid exposure on disrupted CYPs in infants and their anticipated long-term clinical implications. Study Design: DNA methylation levels of CYP genes were analyzed in a cohort of 96 placental tissues using Illumina Infinium MethylationEPIC (850 k) BeadChips. This involved three groups of placental tissues: 32 from mothers with infants exposed to opioids prenatally requiring pharmacologic treatment for NOWS, 32 from mothers with prenatally opioid-exposed infants not needing NOWS treatment, and 32 from unexposed control mothers. Results: The study identified 20 significantly differentially methylated CpG sites associated with 17 distinct CYP genes, with 14 CpGs showing reduced methylation across 14 genes (CYP19A1, CYP1A2, CYP4V2, CYP1B1, CYP24A1, CYP26B1, CYP26C1, CYP2C18, CYP2C9, CYP2U1, CYP39A1, CYP2R1, CYP4Z1, CYP2D7P1 and), while 8 exhibited hypermethylation (CYP51A1, CYP26B1, CYP2R1, CYP2U1, CYP4X1, CYP1A2, CYP2W1, and CYP4V2). Genes such as CYP1A2, CYP26B1, CYP2R1, CYP2U1, and CYP4V2 exhibited both increased and decreased methylation. These genes are crucial for metabolizing eicosanoids, fatty acids, drugs, and diverse substances. Conclusion: The study identified profound methylation changes in multiple CYP genes in the placental tissues relevant to NOWS. This suggests that disruption of DNA methylation patterns in CYP transcripts might play a role in NOWS and may serve as valuable biomarkers, suggesting a future pathway for personalized treatment. Further research is needed to confirm these findings and explore their potential for diagnosis and treatment.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Senthilkumar Sadhasivam
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rupa Radhakrishnan
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, United States
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Science, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Radhakrishna U, Ratnamala U, Jhala DD, Uppala LV, Vedangi A, Patel M, Vadsaria N, Shah S, Saiyed N, Rawal RM, Mercuri SR, Jemec GBE, Damiani G. Hidradenitis suppurativa presents a methylome dysregulation capable to explain the pro-inflammatory microenvironment: Are these DNA methylations potential therapeutic targets? J Eur Acad Dermatol Venereol 2023; 37:2109-2123. [PMID: 37338327 DOI: 10.1111/jdv.19286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/27/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) is a chronic, systemic, inflammatory skin condition with elusive pathogenesis that affects therapeutic intervention directly. OBJECTIVE To characterize epigenetic variations in cytokines genes contributing to HS. METHODS Epigenome-wide DNA methylation profiling with the Illumina Epic array was performed on blood DNA samples from 24 HS patients and 24 age- and sex-matched controls to explore DNA methylation changes in cytokine genes. RESULTS We identified 170 cytokine genes including 27 hypermethylated CpG sites and 143 genes with hypomethylated sites respectively. Hypermethylated genes, including LIF, HLA-DRB1, HLA-G, MTOR, FADD, TGFB3, MALAT1 and CCL28; hypomethylated genes, including NCSTN, SMAD3, IGF1R, IL1F9, NOD2, NOD1, YY1, DLL1 and BCL2 may contribute to the pathogenesis of HS. These genes were enriched in the 117 different pathways (FDR p-values ≤ 0.05), including IL-4/IL-13 pathways and Wnt/β-catenin signalling. CONCLUSIONS The lack of wound healing, microbiome dysbiosis and increased tumour susceptibility are all sustained by these dysfunctional methylomes, hopefully, capable to be targeted in the next future. Since methylome describes and summarizes genetic and environmental contributions, these data may represent a further step towards a feasible precision medicine also for HS patients.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynaecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Uppala Ratnamala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Devendrasinh D Jhala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, India
| | - Lavanya V Uppala
- College of Information Science & Technology, The University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, Nebraska, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON Hospital, A Unit of ICON Krishi Institute Medical Sciences, Visakhapatnam, India
| | | | | | - Sushma Shah
- Department of Obstetrics and Gynaecology, B.J. Medical College, Ahmedabad, India
| | - Nazia Saiyed
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M Rawal
- College of Information Science & Technology, The University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, Nebraska, USA
| | - Santo Raffaele Mercuri
- Unit of Clinical Dermatology, Università Vita-Salute San Raffaele, Milan, Italy
- Italian Center of Precisione Medicine and Chronic Inflammation, Milan, Italy
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
| | - Giovanni Damiani
- Unit of Clinical Dermatology, Università Vita-Salute San Raffaele, Milan, Italy
- Italian Center of Precisione Medicine and Chronic Inflammation, Milan, Italy
- Clinical Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
- Young Dermatologists Italian Network, Milan, Italy
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Radhakrishna U, Nath SK, Uppala LV, Veerappa A, Forray A, Muvvala SB, Metpally RP, Crist RC, Berrettini WH, Mausi LM, Vishweswaraiah S, Bahado-Singh RO. Placental microRNA methylome signatures may serve as biomarkers and therapeutic targets for prenatally opioid-exposed infants with neonatal opioid withdrawal syndrome. Front Genet 2023; 14:1215472. [PMID: 37434949 PMCID: PMC10332887 DOI: 10.3389/fgene.2023.1215472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction: The neonate exposed to opioids in utero faces a constellation of withdrawal symptoms postpartum commonly called neonatal opioid withdrawal syndrome (NOWS). The incidence of NOWS has increased in recent years due to the opioid epidemic. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. Epigenetic variations in microRNAs (miRNAs) and their impact on addiction-related processes is a rapidly evolving area of research. Methods: The Illumina Infinium Methylation EPIC BeadChip was used to analyze DNA methylation levels of miRNA-encoding genes in 96 human placental tissues to identify miRNA gene methylation profiles as-sociated with NOWS: 32 from mothers whose prenatally opioid-exposed infants required pharmacologic management for NOWS, 32 from mothers whose prenatally opioid-exposed infants did not require treat-ment for NOWS, and 32 unexposed controls. Results: The study identified 46 significantly differentially methylated (FDR p-value ≤ 0.05) CpGs associated with 47 unique miRNAs, with a receiver operating characteristic (ROC) area under the curve (AUC) ≥0.75 including 28 hypomethylated and 18 hypermethylated CpGs as potentially associated with NOWS. These dysregulated microRNA methylation patterns may be a contributing factor to NOWS pathogenesis. Conclusion: This is the first study to analyze miRNA methylation profiles in NOWS infants and illustrates the unique role miRNAs might have in diagnosing and treating the disease. Furthermore, these data may provide a step toward feasible precision medicine for NOWS babies as well.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Lavanya V. Uppala
- College of Information Science and Technology, Peter Kiewit Institute, The University of Nebraska at Omaha, Omaha, NE, United States
| | - Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Danville, PA, United States
| | - Richard C. Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wade H. Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Geisinger Clinic, Danville, PA, United States
| | - Lori M. Mausi
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
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Swierkowska J, Vishweswaraiah S, Mrugacz M, Radhakrishna U, Gajecka M. Differential methylation of microRNA encoding genes may contribute to high myopia. Front Genet 2023; 13:1089784. [PMID: 36685896 PMCID: PMC9847511 DOI: 10.3389/fgene.2022.1089784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction: High myopia (HM), an eye disorder with a refractive error ≤-6.0 diopters, has multifactorial etiology with environmental and genetic factors involved. Recent studies confirm the impact of alterations in DNA methylation and microRNAs (miRNAs) on myopia. Here, we studied the combined aspects evaluating to the role of methylation of miRNA encoding genes in HM. Materials and Methods: From the genome-wide DNA methylation data of 18 Polish children with HM and 18 matched controls, we retrieved differentially methylated CG dinucleotides localized in miRNA encoding genes. Putative target genes of the highest-ranked miRNAs were obtained from the miRDB and included in overrepresentation analyses in the ConsensusPathDB. Expression of target genes was assessed using the RNA sequencing data of retinal ARPE-19 cell line. Results: We identified differential methylation of CG dinucleotides in promoter regions of MIR3621, MIR34C, MIR423 (increased methylation level), and MIR1178, MIRLET7A2, MIR885, MIR548I3, MIR6854, MIR675, MIRLET7C, MIR99A (decreased methylation level) genes. Several targets of these miRNAs, e.g. GNAS, TRAM1, CTNNB1, EIF4B, TENM3 and RUNX were previously associated with myopia/HM/refractive error in Europeans in genome-wide association studies. Overrepresentation analyses of miRNAs' targets revealed enrichment in pathways/processes related to eye structure/function, such as axon guidance, transcription, focal adhesion, and signaling pathways of TGF-β, insulin, MAPK and EGF-EGFR. Conclusion: Differential methylation of indicated miRNA encoding genes might influence their expression and contribute to HM pathogenesis via disrupted regulation of transcription of miRNAs' target genes. Methylation of genes encoding miRNAs may be a new direction in research on both the mechanisms determining HM and non-invasive indicators in diagnostics.
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Affiliation(s)
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Malgorzata Mrugacz
- Department of Ophthalmology and Eye Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland,*Correspondence: Marzena Gajecka,
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Desmettre T, Gatinel D, Leveziel N. Épigénétique et myopie : mécanismes et perspectives thérapeutiques. J Fr Ophtalmol 2022; 45:1209-1216. [DOI: 10.1016/j.jfo.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022]
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Ashok A, Pooranawattanakul S, Tai WL, Cho KS, Utheim TP, Cestari DM, Chen DF. Epigenetic Regulation of Optic Nerve Development, Protection, and Repair. Int J Mol Sci 2022; 23:ijms23168927. [PMID: 36012190 PMCID: PMC9408916 DOI: 10.3390/ijms23168927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic factors are known to influence tissue development, functionality, and their response to pathophysiology. This review will focus on different types of epigenetic regulators and their associated molecular apparatus that affect the optic nerve. A comprehensive understanding of epigenetic regulation in optic nerve development and homeostasis will help us unravel novel molecular pathways and pave the way to design blueprints for effective therapeutics to address optic nerve protection, repair, and regeneration.
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Affiliation(s)
- Ajay Ashok
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Sarita Pooranawattanakul
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Wai Lydia Tai
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Kin-Sang Cho
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Tor P. Utheim
- Department of Medical Biochemistry, Oslo University Hospital, 0372 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0372 Oslo, Norway
| | - Dean M. Cestari
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Dong Feng Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Correspondence:
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Swierkowska J, Karolak JA, Vishweswaraiah S, Mrugacz M, Radhakrishna U, Gajecka M. Decreased Levels of DNA Methylation in the PCDHA Gene Cluster as a Risk Factor for Early-Onset High Myopia in Young Children. Invest Ophthalmol Vis Sci 2022; 63:31. [PMID: 36036911 PMCID: PMC9434983 DOI: 10.1167/iovs.63.9.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purpose High myopia (HM), an eye disorder with at least –6.0 diopters refractive error, has a complex etiology with environmental, genetic, and likely epigenetic factors involved. To complement the DNA methylation assessment in children with HM, we analyzed genes that had significantly lower DNA methylation levels. Methods The DNA methylation pattern was studied based on the genome-wide methylation data of 18 Polish children with HM paired with 18 controls. Genes overlapping CG dinucleotides with decreased methylation level in HM cases were assessed by enrichment analyses. From those, genes with CG dinucleotides in promoter regions were further evaluated based on exome sequencing (ES) data of 16 patients with HM from unrelated Polish families, Sanger sequencing data of the studied children, and the RNA sequencing data of human retinal ARPE-19 cells. Results The CG dinucleotide with the most decreased methylation level in cases was identified in a promoter region of PCDHA10 that overlaps intronic regions of PCDHA1–9 of the PCDHA gene cluster in myopia 5q31 locus. Also, two single nucleotide variants, rs200661444, detected in our ES, and rs246073, previously found as associated with a refractive error in a genome-wide association study, were revealed within this gene cluster. Additionally, genes previously linked to ocular phenotypes, myopia-related traits, or loci, including ADAM20, ZFAND6, ETS1, ABHD13, SBSPON, SORBS2, LMOD3, ATXN1, and FARP2, were found to have decreased methylation. Conclusions Alterations in the methylation pattern of specific CG dinucleotides may be associated with early-onset HM, so this could be used to develop noninvasive biomarkers of HM in children and adolescents.
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Affiliation(s)
| | - Justyna A Karolak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States
| | - Malgorzata Mrugacz
- Department of Ophthalmology and Eye Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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11
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Brown DM, Mazade R, Clarkson-Townsend D, Hogan K, Datta Roy PM, Pardue MT. Candidate pathways for retina to scleral signaling in refractive eye growth. Exp Eye Res 2022; 219:109071. [PMID: 35447101 PMCID: PMC9701099 DOI: 10.1016/j.exer.2022.109071] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/25/2022] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
The global prevalence of myopia, or nearsightedness, has increased at an alarming rate over the last few decades. An eye is myopic if incoming light focuses prior to reaching the retinal photoreceptors, which indicates a mismatch in its shape and optical power. This mismatch commonly results from excessive axial elongation. Important drivers of the myopia epidemic include environmental factors, genetic factors, and their interactions, e.g., genetic factors influencing the effects of environmental factors. One factor often hypothesized to be a driver of the myopia epidemic is environmental light, which has changed drastically and rapidly on a global scale. In support of this, it is well established that eye size is regulated by a homeostatic process that incorporates visual cues (emmetropization). This process allows the eye to detect and minimize refractive errors quite accurately and locally over time by modulating the rate of elongation of the eye via remodeling its outermost coat, the sclera. Critically, emmetropization is not dependent on post-retinal processing. Thus, visual cues appear to influence axial elongation through a retina-to-sclera, or retinoscleral, signaling cascade, capable of transmitting information from the innermost layer of the eye to the outermost layer. Despite significant global research interest, the specifics of retinoscleral signaling pathways remain elusive. While a few pharmacological treatments have proven to be effective in slowing axial elongation (most notably topical atropine), the mechanisms behind these treatments are still not fully understood. Additionally, several retinal neuromodulators, neurotransmitters, and other small molecules have been found to influence axial length and/or refractive error or be influenced by myopigenic cues, yet little progress has been made explaining how the signal that originates in the retina crosses the highly vascular choroid to affect the sclera. Here, we compile and synthesize the evidence surrounding three of the major candidate pathways receiving significant research attention - dopamine, retinoic acid, and adenosine. All three candidates have both correlational and causal evidence backing their involvement in axial elongation and have been implicated by multiple independent research groups across diverse species. Two hypothesized mechanisms are presented for how a retina-originating signal crosses the choroid - via 1) all-trans retinoic acid or 2) choroidal blood flow influencing scleral oxygenation. Evidence of crosstalk between the pathways is discussed in the context of these two mechanisms.
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Affiliation(s)
- Dillon M Brown
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA; Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA
| | - Reece Mazade
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA; Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA
| | - Danielle Clarkson-Townsend
- Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA, 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA; Gangarosa Department of Environmental Health, Emory University, 1518 Clifton Rd, Atlanta, GA, 30322, USA
| | - Kelleigh Hogan
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA; Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA
| | - Pooja M Datta Roy
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA; Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA
| | - Machelle T Pardue
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA; Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Healthcare System, 1670 Clairmont Rd, Atlanta, GA, 30033, USA.
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12
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Thomson K, Game J, Karouta C, Morgan IG, Ashby R. Correlation between small-scale methylation changes and gene expression during the development of myopia. FASEB J 2021; 36:e22129. [PMID: 34958689 DOI: 10.1096/fj.202101487r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022]
Abstract
Visually induced changes in the expression of early growth response-1 (EGR1), FBJ osteosarcoma oncogene (FOS), and NGFI-A binding protein-2 (NAB2) appear to form a part of a retinal network fundamental to ocular growth regulation, and thus, the development of myopia (short-sightedness). However, it is unclear how environmental (visual) cues are translated into these molecular changes. One possibility is through epigenetic modifications such as DNA methylation, a known regulator of such processes. By sequencing bisulfite-converted DNA amplicons, this study examined whether changes in DNA methylation occur within specific regulatory and promoter regions of EGR1, FOS, and NAB2 during the periods of increased and decreased ocular growth in chicks. Visually induced changes in ocular growth rates were associated with single-point, but not large-scale, shifts in methylation levels within the investigated regions. Analysis of methylation pattern variability (entropy) demonstrated that the observed methylation changes are occurring within small subpopulations of retinal cells. This concurs with previous observations that EGR1 and FOS are differentially regulated at the peptide level within specific retinal cell types. Together, the findings of this study support a potential role for DNA methylation in the translation of external visual cues into molecular changes critical for ocular growth regulation and myopia development.
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Affiliation(s)
- Kate Thomson
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Jeremy Game
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Cindy Karouta
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Ian G Morgan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Regan Ashby
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
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13
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Karouta C, Kucharski R, Hardy K, Thomson K, Maleszka R, Morgan I, Ashby R. Transcriptome-based insights into gene networks controlling myopia prevention. FASEB J 2021; 35:e21846. [PMID: 34405458 DOI: 10.1096/fj.202100350rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022]
Abstract
Myopia (short-sightedness), usually caused by excessive elongation of the eye during development, has reached epidemic proportions worldwide. In animal systems including the chicken model, several treatments have been shown to inhibit ocular elongation and experimental myopia. Although diverse in their apparent mechanism of action, each one leads to a reduction in the rate of ocular growth. We hypothesize that a defined set of retinal molecular changes may underlie growth inhibition, irrespective of the treatment agent used. Accordingly, across five well-established but diverse methods of inhibiting myopia, significant overlap is seen in the retinal transcriptome profile (transcript levels and alternative splicing events) in chicks when analyzed by RNA-seq. Within the two major pathway networks enriched during growth inhibition, that of cell signaling and circadian entrainment, transcription factors form the largest functional grouping. Importantly, a large percentage of those genes forming the defined retinal response are downstream targets of the transcription factor EGR1 which itself shows a universal response to all five growth-inhibitory treatments. This supports EGR1's previously implicated role in ocular growth regulation. Finally, by contrasting our data with human linkage and GWAS studies on refractive error, we confirm the applicability of our study to the human condition. Together, these findings suggest that a universal set of transcriptome changes, which sit within a well-defined retinal network that cannot be bypassed, is fundamental to growth regulation, thus paving a way for designing novel targets for myopia therapies.
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Affiliation(s)
- Cindy Karouta
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Robert Kucharski
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Kristine Hardy
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kate Thomson
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ian Morgan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Regan Ashby
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
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14
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Summers JA, Schaeffel F, Marcos S, Wu H, Tkatchenko AV. Functional integration of eye tissues and refractive eye development: Mechanisms and pathways. Exp Eye Res 2021; 209:108693. [PMID: 34228967 DOI: 10.1016/j.exer.2021.108693] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/16/2022]
Abstract
Refractive eye development is a tightly coordinated developmental process. The general layout of the eye and its various components are established during embryonic development, which involves a complex cross-tissue signaling. The eye then undergoes a refinement process during the postnatal emmetropization process, which relies heavily on the integration of environmental and genetic factors and is controlled by an elaborate genetic network. This genetic network encodes a multilayered signaling cascade, which converts visual stimuli into molecular signals that guide the postnatal growth of the eye. The signaling cascade underlying refractive eye development spans across all ocular tissues and comprises multiple signaling pathways. Notably, tissue-tissue interaction plays a key role in both embryonic eye development and postnatal eye emmetropization. Recent advances in eye biometry, physiological optics and systems genetics of refractive error have significantly advanced our understanding of the biological processes involved in refractive eye development and provided a framework for the development of new treatment options for myopia. In this review, we summarize the recent data on the mechanisms and signaling pathways underlying refractive eye development and discuss new evidence suggesting a wide-spread signal integration across different tissues and ocular components involved in visually guided eye growth.
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Affiliation(s)
- Jody A Summers
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Frank Schaeffel
- Section of Neurobiology of the Eye, Ophthalmic Research Institute, University of Tuebingen, Tuebingen, Germany; Myopia Research Group, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - Susana Marcos
- Instituto de Óptica "Daza de Valdés", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Hao Wu
- Department of Ophthalmology, Columbia University, New York, USA
| | - Andrei V Tkatchenko
- Department of Ophthalmology, Columbia University, New York, USA; Department of Pathology and Cell Biology, Columbia University, New York, USA.
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15
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Retinal Stem Cell 'Retirement Plans': Growth, Regulation and Species Adaptations in the Retinal Ciliary Marginal Zone. Int J Mol Sci 2021; 22:ijms22126528. [PMID: 34207050 PMCID: PMC8234741 DOI: 10.3390/ijms22126528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
The vertebrate retina develops from a specified group of precursor cells that adopt distinct identities and generate lineages of either the neural retina, retinal pigmented epithelium, or ciliary body. In some species, including teleost fish and amphibians, proliferative cells with stem-cell-like properties capable of continuously supplying new retinal cells post-embryonically have been characterized and extensively studied. This region, termed the ciliary or circumferential marginal zone (CMZ), possibly represents a conserved retinal stem cell niche. In this review, we highlight the research characterizing similar CMZ-like regions, or stem-like cells located at the peripheral margin, across multiple different species. We discuss the proliferative parameters, multipotency and growth mechanisms of these cells to understand how they behave in vivo and how different molecular factors and signalling networks converge at the CMZ niche to regulate their activity. The evidence suggests that the mature retina may have a conserved propensity for homeostatic growth and plasticity and that dysfunction in the regulation of CMZ activity may partially account for dystrophic eye growth diseases such as myopia and hyperopia. A better understanding of the properties of CMZ cells will enable important insight into how an endogenous generative tissue compartment can adapt to altered retinal physiology and potentially even restore vision loss caused by retinal degenerative conditions.
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16
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Tkatchenko TV, Tkatchenko AV. Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection. BMC Med Genomics 2021; 14:153. [PMID: 34107987 PMCID: PMC8190860 DOI: 10.1186/s12920-021-01005-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. METHODS Here, we used genome-wide RNA-sequencing to conduct analysis of the retinal gene expression network underlying contrast perception and refractive eye development. RESULTS We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. CONCLUSIONS Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.
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Affiliation(s)
| | - Andrei V. Tkatchenko
- Department of Ophthalmology, Columbia University, New York, NY USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY USA
- Edward S. Harkness Eye Institute, Research Annex Room 415, 635 W. 165th Street, New York, NY 10032 USA
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17
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Jong M, Jonas JB, Wolffsohn JS, Berntsen DA, Cho P, Clarkson-Townsend D, Flitcroft DI, Gifford KL, Haarman AEG, Pardue MT, Richdale K, Sankaridurg P, Tedja MS, Wildsoet CF, Bailey-Wilson JE, Guggenheim JA, Hammond CJ, Kaprio J, MacGregor S, Mackey DA, Musolf AM, Klaver CCW, Verhoeven VJM, Vitart V, Smith EL. IMI 2021 Yearly Digest. Invest Ophthalmol Vis Sci 2021; 62:7. [PMID: 33909031 PMCID: PMC8088231 DOI: 10.1167/iovs.62.5.7] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/24/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose The International Myopia Institute (IMI) Yearly Digest highlights new research considered to be of importance since the publication of the first series of IMI white papers. Methods A literature search was conducted for articles on myopia between 2019 and mid-2020 to inform definitions and classifications, experimental models, genetics, interventions, clinical trials, and clinical management. Conference abstracts from key meetings in the same period were also considered. Results One thousand articles on myopia have been published between 2019 and mid-2020. Key advances include the use of the definition of premyopia in studies currently under way to test interventions in myopia, new definitions in the field of pathologic myopia, the role of new pharmacologic treatments in experimental models such as intraocular pressure-lowering latanoprost, a large meta-analysis of refractive error identifying 336 new genetic loci, new clinical interventions such as the defocus incorporated multisegment spectacles and combination therapy with low-dose atropine and orthokeratology (OK), normative standards in refractive error, the ethical dilemma of a placebo control group when myopia control treatments are established, reporting the physical metric of myopia reduction versus a percentage reduction, comparison of the risk of pediatric OK wear with risk of vision impairment in myopia, the justification of preventing myopic and axial length increase versus quality of life, and future vision loss. Conclusions Large amounts of research in myopia have been published since the IMI 2019 white papers were released. The yearly digest serves to highlight the latest research and advances in myopia.
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Affiliation(s)
- Monica Jong
- Discipline of Optometry and Vision Science, University of Canberra, Canberra, Australian Capital Territory, Australia
- Brien Holden Vision Institute, Sydney, New South Wales, Australia
- School of Optometry and Vision Science, School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Jost B. Jonas
- Department of Ophthalmology Medical Faculty Mannheim, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - James S. Wolffsohn
- Optometry and Vision Science Research Group, Aston University, Birmingham, United Kingdom
| | - David A. Berntsen
- The Ocular Surface Institute, College of Optometry, University of Houston, Houston, Texas, United States
| | - Pauline Cho
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Danielle Clarkson-Townsend
- Center for Visual and Neurocognitive Rehabilitation, Atlanta VA Healthcare System, Decatur, Georgia, United States
- Gangarosa Department of Environmental Health, Emory University, Atlanta, Georgia, United States
| | - Daniel I. Flitcroft
- Department of Ophthalmology, Children's University Hospital, Dublin, Ireland
| | - Kate L. Gifford
- Myopia Profile Pty Ltd, Brisbane, Queensland, Australia
- Queensland University of Technology (QUT) School of Optometry and Vision Science, Kelvin Grove, Queensland, Australia
| | - Annechien E. G. Haarman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Machelle T. Pardue
- Center for Visual and Neurocognitive Rehabilitation, Atlanta VA Healthcare System, Decatur, Georgia, United States
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
| | - Kathryn Richdale
- College of Optometry, University of Houston, Houston, Texas, United States
| | - Padmaja Sankaridurg
- Brien Holden Vision Institute, Sydney, New South Wales, Australia
- School of Optometry and Vision Science, School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Milly S. Tedja
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Jeremy A. Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Christopher J. Hammond
- Section of Academic Ophthalmology, School of Life Course Sciences, King's College London, London, United Kingdom
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Anthony M. Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Caroline C. W. Klaver
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Earl L. Smith
- College of Optometry, University of Houston, Houston, Texas, United States
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18
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Wang H, Li J, Wang S, Lu X, Zhang G, Zhuang Y, Li L, Wang W, Lin P, Chen C, Wang H, Chen Q, Jiang Y, Qu J, Xu L. Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia. Brief Bioinform 2021; 22:6217725. [PMID: 33834194 DOI: 10.1093/bib/bbab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/12/2022] Open
Abstract
Transcriptional regulation is associated with complicated mechanisms including multiple molecular interactions and collaborative drive. Long noncoding RNAs (lncRNAs) have highly structured characteristics and play vital roles in the regulation of transcription in organisms. However, the specific contributions of conformation feature and underlying molecular mechanisms are still unclear. In the present paper, a hypothesis regarding molecular structure effect is presented, which proposes that lncRNAs fold into a complex spatial architecture and act as a skeleton to recruit transcription factors (TF) targeted binding, and which is involved in cooperative regulation. A candidate set of TF-lncRNA coregulation was constructed, and it was found that structural accessibility affected molecular binding force. In addition, transcription factor binding site (TFBS) regions of myopia-related lncRNA transcripts were disturbed, and it was discovered that base mutations affected the occurrence of significant molecular allosteric changes in important elements and variable splicing regions, mediating the onset and development of myopia. The results originated from structureomics and interactionomics and created conditions for systematic research on the mechanisms of structure-mediated TF-lncRNA coregulation in transcriptional regulation. Finally, these findings will help further the understanding of key regulatory roles of molecular allostery in cell physiological and pathological processes.
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Affiliation(s)
- Hong Wang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University and cooperates with College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Jing Li
- College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Xiaoyan Lu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Guosi Zhang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Youyuan Zhuang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Liansheng Li
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Wencan Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Chong Chen
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Hao Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Qi Chen
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Jia Qu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Liangde Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
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19
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Radhakrishna U, Vishweswaraiah S, Uppala LV, Szymanska M, Macknis J, Kumar S, Saleem-Rasheed F, Aydas B, Forray A, Muvvala SB, Mishra NK, Guda C, Carey DJ, Metpally RP, Crist RC, Berrettini WH, Bahado-Singh RO. Placental DNA methylation profiles in opioid-exposed pregnancies and associations with the neonatal opioid withdrawal syndrome. Genomics 2021; 113:1127-1135. [PMID: 33711455 DOI: 10.1016/j.ygeno.2021.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/29/2020] [Accepted: 03/02/2021] [Indexed: 12/11/2022]
Abstract
Opioid abuse during pregnancy can result in Neonatal Opioid Withdrawal Syndrome (NOWS). We investigated genome-wide methylation analyses of 96 placental tissue samples, including 32 prenatally opioid-exposed infants with NOWS who needed therapy (+Opioids/+NOWS), 32 prenatally opioid-exposed infants with NOWS who did not require treatment (+Opioids/-NOWS), and 32 prenatally unexposed controls (-Opioids/-NOWS, control). Statistics, bioinformatics, Artificial Intelligence (AI), including Deep Learning (DL), and Ingenuity Pathway Analyses (IPA) were performed. We identified 17 dysregulated pathways thought to be important in the pathophysiology of NOWS and reported accurate AI prediction of NOWS diagnoses. The DL had an AUC (95% CI) =0.98 (0.95-1.0) with a sensitivity and specificity of 100% for distinguishing NOWS from the +Opioids/-NOWS group and AUCs (95% CI) =1.00 (1.0-1.0) with a sensitivity and specificity of 100% for distinguishing NOWS versus control and + Opioids/-NOWS group versus controls. This study provides strong evidence of methylation dysregulation of placental tissue in NOWS development.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA.
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Lavanya V Uppala
- College of Information Science & Technology, University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, NE, USA
| | - Marta Szymanska
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | | | - Sandeep Kumar
- Department of Pathology, Beaumont Health System, Royal Oak, MI, USA
| | - Fozia Saleem-Rasheed
- Department of Newborn Medicine, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, USA
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | | | - Nitish K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, NE, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, NE, USA
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Raghu P Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Richard C Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Geisinger Clinic, Danville, PA, USA
| | - Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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20
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Yang N, Bai J, Liu L. Low concentration atropine combined with orthokeratology in the treatment of axial elongation in children with myopia: A meta-analysis. Eur J Ophthalmol 2021; 32:221-228. [PMID: 33678055 DOI: 10.1177/1120672121998903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To evaluate the effect of low concentration atropine combined with Orthokeratology (OK) lens compared with the OK lens on the changes of axial length in children with moderate and low myopia by meta-analysis. METHODS Databases such as PubMed, Web of Science, Embase, and Cochrane Library were comprehensively searched to collect related studies on atropine combined with the OK lens in the treatment of children with moderate and low myopia. The retrieval time was from the establishment of the database to December 2020. The standardized mean difference (SMD) and its 95% confidence interval (CI) were selected as the effect to analyze the changes of the axial length of the eye axis in children with low and moderate myopia treated with low concentration atropine combined with OK lens. RESULTS A total of eight articles were included in this study. Compared with OK lens treatment, low concentration atropine combined with the OK lens significantly slowed down the axial elongation of low and moderate myopia, SMD = -0.68(95% CI: -0.86--0.50, p < 0.05). According to the subgroup analysis of treatment time, when the treatment time was less than or equal to 6 months, SMD = -0.63(95% CI: -0.88--0.37, p < 0.05), when the treatment time was 1 year, SMD = -0.76(95% CI: -1.08--0.43, p < 0.05), and when the treatment time was 2 years, SMD = -0.69(95% CI: -1.07--0.31, p < 0.05). CONCLUSION Low concentration atropine combined with the OK lens is more effective than the OK lens in the treatment of children with low to moderate myopia in reducing axial elongation.
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Affiliation(s)
- Ning Yang
- Your Bright Eye Clinic of Chengdu Hi-tech Zone, Chengdu, Sichuan, China
| | | | - Li Liu
- Your Bright Eye Clinic of Chengdu Hi-tech Zone, Chengdu, Sichuan, China
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21
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Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. Adv Med Sci 2021; 66:192-198. [PMID: 33711669 DOI: 10.1016/j.advms.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE High myopia (HM) is an eye disorder with both environmental and genetic factors involved. Many genetic factors responsible for HM were recognized worldwide, but little is known about genetic variants underlying HM in Central Europe. Thus, the aim of this study was to identify rare sequence variants involved in HM in families from Central Europe to better understand the genetic basis of HM. MATERIALS AND METHODS We assessed 17 individuals from 7 unrelated Central European families with hereditary HM using exome sequencing (ES). Segregation of selected variants in other available family members was performed using Sanger sequencing. RESULTS Detected 73 rare variants were selected for verification. We observed 2 missense variants, c.938C>T in SLC35E2B - encoding solute carrier family 35 member E2B, and c.1642G>C in FLRT3 - encoding fibronectin leucine rich transmembrane protein, segregating with HM in one family. CONCLUSIONS FLRT3 and/or SLC35E2B could represent disease candidate genes and identified sequence variants might be responsible for HM in the studied family.
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22
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Geng C, Li Y, Guo F, Wang J, Yue Y, Zhou K, Wei R, Zhang Y. RNA sequencing analysis of long non-coding RNA expression in ocular posterior poles of guinea pig myopia models. Mol Vis 2020; 26:117-134. [PMID: 32180678 PMCID: PMC7058432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 10/27/2022] Open
Abstract
Purpose To detect the differential expression of long non-coding RNAs (lncRNAs) in the ocular posterior poles of two guinea pig myopia models and explore the pathogenic role of lncRNAs in myopia. Methods Form-deprived myopia (FDM) and lens-induced myopia (LIM) models were induced in guinea pig right eyes by wearing a translucent latex balloon head mask and a -10.00 diopter (D) lens, respectively. Ocular biometric parameters were measured biweekly. At 6 weeks after the induction of myopia, the guinea pig eyeballs were processed for hematoxylin and eosin staining to examine the ocular morphology. The ocular posterior poles from the normal control, FDM, and LIM groups were collected to analyze the differential expression of lncRNAs between the groups with high-throughput RNA sequencing (RNA-seq). Further, the lncRNA-mRNA colocation network was delineated to predict the functions of the differentially expressed lncRNAs. Last, Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the colocated mRNAs of the differentially expressed lncRNAs. Additionally, the expression of the most differentially expressed lncRNAs in the myopia-induced eyes and the contralateral eyes was validated with quantitative real-time PCR (qPCR). Results Compared with the normal controls and the contralateral eyes, the myopia-induced eyes in the FDM and LIM groups exhibited decreased scleral and choroidal thicknesses, reduced refraction, and increased ocular axial length but without changes in the corneal curvature radius at 6 weeks after myopia was induced. RNA-seq showed that 372 and 247 lncRNAs were differentially expressed in the FDM and LIM groups, respectively, in comparison to the normal counterparts. There were 380 differentially expressed lncRNAs in the LIM group compared to the FDM group. The GO and KEGG analyses showed that the colocated mRNAs of the differentially expressed lncRNAs were enriched in cellular components such as the extracellular matrix (ECM) structural constituent; in molecular functions such as kinase activity, metabolism, and growth; as well as in pathways including ECM-receptor interaction, glycosaminoglycan degradation, and mucin type O-Glycan biosynthesis. The expression patterns of the selected lncRNAs were verified with qPCR. Conclusions High-throughput RNA-seq revealed previously undescribed lncRNA expression profiling in guinea pig FDM and LIM models. These results may shed light on the molecular pathogenesis of myopia and provide clues for interventional targets for this highly prevalent visual disorder.
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